UCL Cancer Institute

Medical genomics


Medical Genomics Logo

Group Leader: Professor Stephan Beck


The laboratory has broad interests in the genomics and epigenomics of phenotypic plasticity in health and disease. In addition to genetic variations, we study epigenetic variations such as DNA methylation, histone modifications and microRNAs and how they modulate genome function. Central to our research is the development of systems approaches for integration of multi-dimensional data and their application to epigenome-wide association studies (EWAS) in cancer and other common diseases to advance translational, regenerative and personalized medicine. The Medical Genomics Group offers state-of-the-art facilities and a stimulating environment for graduate and post-doctoral training.







Group Members



 

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Name: James Barrett

Position: Research Associate

Email: regmjeb(at)ucl.ac.uk



Further Details:
 I am interested in the statistical analysis of biomedical data. The integration of multiple genomic datasets, dimensionality reduction techniques, Bayesian methods, and survival analysis (especially competing risks) are of particular interest. I am attempting to derive low dimensional biomarkers from genomic data that are useful for predicting clinical outcomes, making accurate diagnoses, or determining drug response. I am developing new mathematical and statistical tools to do this. I joined the Medical Genomics group at UCL in 2014 and am collaborating with the OncoTrack consortium. I obtained a PhD in Applied Mathematics from King’s College London in 2014 (with Ton Coolen at the Institute for Mathematical and Molecular Biomedicine). I also completed an MSc in Mathematics at King’s College London (in the Disordered Systems Group). My undergraduate degree was in Theoretical Physics at Trinity College Dublin

 



 

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Name: Charles Breeze

Position: PhD Student

Email: c.breeze(at)ucl.ac.uk

Tel: +44-20-76790997

Further Details:
 I studied Biochemistry and Bioinformatics at the University of Navarra, Spain, graduating in 2013. During my studies at university I was awarded two research placements at the University of Oxford, with Prof. Charles Lawrie (Ballabio et al, 2012) and Prof. Alison Banham (LLR studentship). I have joined Prof. Stephan Beck’s group with a Marie Curie PhD fellowship to work on the study of the epigenetics of complex traits and diseases, as part of the EpiTRAIN Initial Training Network.

 



 

lbutcher
Name: Lee Butcher

Position: Research Associate

Email: l.butcher(at)ucl.ac.uk

Tel: +44-20-76796004

Further Details:
 I graduated from Sussex University in 2001 with a BSc in Experimental Psychology and an appetite for the genetic basis of psychological traits. In 2006 I completed my PhD under the supervision of Professor Robert Plomin at the Institute of Psychiatry (King's College London) where I co-developed a high-throughput, genome-wide allelotyping method. Toward the end of my time at the IoP, a spate of high-powered genome-wide association studies (GWAS) appeared that indicated that single SNP effects in common complex disease were small but ubiquitous. This led me into epigenetics, which, I feel, may contribute more profoundly to human health and disease than solely sequence-based approaches. In early 2008 I joined Professor Beck's lab to establish a high-throughput DNA methylation pipeline."

 



 

pawan
Name: Pawan Dhami

Position: Research Associate

Email: pawan.dhami(at)ucl.ac.uk

Tel: +44-20-76790997

Further Details:
 After completing my post graduation studies in India in the field of Human Genetics, I moved to the UK to pursue a career in research. Subsequently, I completed my PhD in 2006 under the supervision of Dr. Dave Vetrie based at the Sanger Institute, Cambridge. My PhD thesis involved elucidation of DNA-protein interactions using ChIP-chip to study the transcriptional regulation of SCL gene during haematopoietic development. I also used ChIP-chip assay to build maps of DNA-protein interactions at a genome-wide scale in the human and mouse genomes to identify and elucidate various classes of cis-regulatory functional elements, e.g. promoters, enhancers, insulators etc. and link these functional elements to biological processes. In May 2008, I joined Prof. Stephan Beck's lab to understand how DNA methylation plays a role in vertebrate development.

 



 

andrew feber
Name: Andrew Feber

Position: Research Associate

Email: a.feber(at)ucl.ac.uk

Tel: +44-20-76790963

Further Details:
 I completed my BSc (Hons) degree at the University of Newcastle Upon Tyne. In 2001 I joined the Institute of Cancer Research, where under the supervision of Prof. Colin Cooper I carried out my PhD, investigating the genomic alterations associated with the development and progression of urological cancers. In September 2005 I joined the laboratory of Dr. Tony Godfrey at Mount Sinai Medical School, New York, to start my postdoctoral training. During my time in New York I worked on the integration of high resolution genomic copy number, gene expression and miRNA expression data to define molecular signatures associated with esophageal cancer patient survival and to identify novel therapeutic targets. In March 2008, I returned to the UK to join the laboratory of Prof. Stephan Beck, at the UCL Cancer Institute, London, to investigate the role of methylation in the development and progression of cancer.

 



 

Anna Karpathakis Name: Anna Karpathakis

Position: Clinical Research Fellow

Email: a.karpahtakis(at)ucl.ac.uk

Tel: +44-20-76790997

Further Details:
 Anna is a clinical research fellow undertaking a PhD in the molecular characterisation of gastrointestinal neuroendocrine tumours.

 



 

Anna Koeferle
Name: Anna Koeferle

Position: PhD student

Email: a.koeferle(at)ucl.ac.uk

Tel: +44-20-76790963

Further Details:
I completed an undergraduate degree in Biochemistry at the University of Oxford in 2012. My dissertation project, which I undertook in Prof. Peter Cook’s lab at the Sir William Dunn School of Pathology, focused on a model in which transcription occurs in ‘specialized transcription factories’. I attempted to test this model through targeted manipulation of a well-characterised gene loop using a zinc-finger nuclease. In September 2013, I joined Prof. Stephan Beck’s lab in order to commence my PhD, for which I receive funding from CR-UK. I have a general interest in how epigenetic changes contribute to tumorigenesis and plan to use a TALE/CRISPR-based system for targeted epigenetic reprogramming of cancer cells.

 



 

elibertini
Name: Emanuele Libertini

Position: Research Associate

Email: emanuele.libertini(at)ucl.ac.uk

Tel: +44-20-76790999

Further Details:
Graduating from the University of London with a PhD in Bioinformatics in 2010, I have two undergraduate degrees: a BSc in Biology (York) and a BA in Creative Writing (Brunel). My PhD was focused on building a gene network using multiple types of data, modelling stress-induced hormone-driven responses in Arabidopsis. In 2010-11, as a UCL teaching fellow, I taught a Biology course in Astana, including lectures, tutorials and practicals (laboratory and computer-based). As a post-doc, my work at Institut Pasteur Paris has brought me in close collaboration with the bacterial-human cell interaction group led by Pascale Cossart. Based at the Epigenomics and Transcriptomics unit (PF2) led by Jean-Yves Coppé, I have been working as key developer of workflows for the analysis of sequencing data, focussing on DNA methylation, protein occupacy and transcription. The EpiLis project (led by Helene Bierne) has been my main focus: working with mammalian cells, developing an insight onto chromatin remodellers and DNA methylation within bacterial infection-induced epigenetic pathways. I joined Stephan Beck's group in January 2014 to contribute to the next generation sequencing analysis and work as resident computational biologist.

 



 

Dirk Paul
Name: Dirk Paul

Position: Research Associate

Email: d.paul(at)ucl.ac.uk

Tel: +44-20-76796004

Further Details:
 I graduated with a BSc and MSc in Life Science from the University of Konstanz, Germany. During my studies at university, I participated in the National University of Singapore Exchange Programme. I worked on complex diseases, such as cirrhosis at the Biopolis in Singapore, and asthma at Boehringer Ingelheim. For my Master's thesis, I worked on the development of a novel approach to targeted high-throughput DNA sequencing at the Wellcome Trust Centre for Human Genetics at the University of Oxford. Until October 2012, I was on a Marie Curie PhD fellowship at the Wellcome Trust Sanger Institute and the University of Cambridge, where I focused on the functional follow-up of genome-wide association study signals. I applied experimental and computational approaches to aid the identification of functional variants underlying association signals for haematological traits and coronary artery disease. In November 2012, I joined Stephan Beck’s group to investigate the role of epigenetic variation in the aetiology of type 1 diabetes in collaboration with the BLUEPRINT consortium.

 



 

Ben Powell
Name: Chris Pipinikas

Position: Research Associate

Email:c.pipinikas(at)ucl.ac.uk

Tel:

 

 



 

Ben Powell
Name: Benjamin Powell

Position: PhD Student

Email:benjamin.powell.09(at)ucl.ac.uk

Tel:

 

 



 

Sabrina Stewart
Name: Sabrina Stewart

Position: PhD student

Email: sabrina.stewart.10(at)ucl.ac.uk

Tel: +44-20-76790999

 



 

Christina Thirlwell Name: Christina Thirlwell

Position: Cancer Research UK Clinician Scientist and Senior Lecturer in Medical Oncology

Email: christina.thirlwell(at)ucl.ac.uk

Tel: +44-20-76790997

Further Details:
  I graduated in Medicine at UCL in 1997 having undertaken an integrated BSc in Immunology in 1994. I went on to train in Medical Oncology and undertook my PhD with Prof. Ian Tomlinson at the Cancer Research UK London Research Institute in colorectal cancer genetics. I completed my clinical training in Medical Oncology  whilst furthering my research interests in cancer epigenetics  between 2008 and 2010 as post-doc in Stephan Becks lab at the UCL Cancer Institute. In 2010 I started my first Clinician Scientist post and currently work as a Consultant in Medical Oncology at the Royal Free Hospital specialising in Neuroenodocrine Tumours – where we are a European Centre of Excellence. I also treat Hepatobiliiary cancer. I now have a post-doc Chris Pipinikas and PhD student Anna Karpathakis working with me in the lab where we are performing large-scale integrated genomic analysis of Neuroendocrine tumours.  Our ultimate aim is to further our understanding of the biology of these tumours whilst identifying and validating novel biomarkers. 

 






Past Members



Paul Guilhamon
Tiffany Morris
Liselotte Backdahl
Christopher Bell
Helena Caren
Penny Coggill
Harpreet Dibra
Ivo Gut
Karen Halls
Christoph Heller
Marlis Herbeth
Roger Horton
Fara Khurshid
Marina Kouyialis
Matthias Lechner
Marcos Miretti
Adele Murrell
William Newell
Karen Novik
Elizabeth Radley
Vardhman Rakyan
Vikki Rand
Jennifer Sambrook
Melanie Stammers
Stefan Stricker
Andrew Teschendorff
Andrew Theaker
Eleni Tomazou
Gareth Wilson
Ruth Younger



 

Stephan Beck

Stephan Beck, PhD FMedSci
Prof of Medical Genomics
UCL Cancer Institute
University College London
Paul OíGorman Building
72 Huntley Street
London WC1E 6BT, UK
Tel: +44-20-7679-0964
s.beck(at)ucl.ac.uk